Examples with DocumentFormatException gate.util.DocumentFormatException used on opensource projects

Example 1 with DocumentFormatException

use of gate.util.DocumentFormatException in project gate-core by GateNLP.

the class XmlDocumentFormat method unpackMarkup.

// unpackMarkup
/**
 * Unpack the markup in the document. This converts markup from the
 * native format (e.g. XML) into annotations in GATE format. Uses the
 * markupElementsMap to determine which elements to convert, and what
 * annotation type names to use. If the document was created from a
 * String, then is recomandable to set the doc's sourceUrl to <b>null</b>.
 * So, if the document has a valid URL, then the parser will try to
 * parse the XML document pointed by the URL.If the URL is not valid,
 * or is null, then the doc's content will be parsed. If the doc's
 * content is not a valid XML then the parser might crash.
 *
 * @param doc The gate document you want to parse. If
 *          <code>doc.getSourceUrl()</code> returns <b>null</b>
 *          then the content of doc will be parsed. Using a URL is
 *          recomended because the parser will report errors corectlly
 *          if the XML document is not well formed.
 */
@Override
public void unpackMarkup(Document doc, RepositioningInfo repInfo, RepositioningInfo ampCodingInfo) throws DocumentFormatException {
    if ((doc == null) || (doc.getSourceUrl() == null && doc.getContent() == null)) {
        throw new DocumentFormatException("GATE document is null or no content found. Nothing to parse!");
    }
    // End if
    // Create a status listener
    StatusListener statusListener = new StatusListener() {

        @Override
        public void statusChanged(String text) {
            // This is implemented in DocumentFormat.java and inherited here
            fireStatusChanged(text);
        }
    };
    // determine whether we have a GATE format XML document or another
    // kind
    String content = doc.getContent().toString();
    if (content.length() > 2048) {
        content = content.substring(0, 2048);
    }
    boolean gateFormat = isGateXmlFormat(content);
    if (gateFormat) {
        unpackGateFormatMarkup(doc, statusListener);
    } else {
        unpackGeneralXmlMarkup(doc, repInfo, ampCodingInfo, statusListener);
    }
}

Example 2 with DocumentFormatException

use of gate.util.DocumentFormatException in project gate-core by GateNLP.

the class XmlDocumentFormat method unpackGateFormatMarkup.

/**
 * Unpacks markup in the GATE-specific standoff XML markup format.
 *
 * @param doc the document to process
 * @param statusListener optional status listener to receive status
 *          messages
 * @throws DocumentFormatException if a fatal error occurs during
 *           parsing
 */
private void unpackGateFormatMarkup(Document doc, StatusListener statusListener) throws DocumentFormatException {
    boolean docHasContentButNoValidURL = hasContentButNoValidUrl(doc);
    try {
        Reader inputReader = null;
        InputStream inputStream = null;
        XMLStreamReader xsr = null;
        if (docHasContentButNoValidURL) {
            inputReader = new StringReader(doc.getContent().toString());
            xsr = getInputFactory().createXMLStreamReader(inputReader);
        } else if (doc instanceof TextualDocument) {
            String encoding = ((TextualDocument) doc).getEncoding();
            // Don't strip BOM on XML.
            inputReader = new InputStreamReader(doc.getSourceUrl().openStream(), encoding);
            // create stream reader with the URL as system ID, to support
            // relative URLs to e.g. DTD or external entities
            xsr = getInputFactory().createXMLStreamReader(doc.getSourceUrl().toExternalForm(), inputReader);
        } else {
            // not a TextualDocument, so let parser determine encoding
            inputStream = doc.getSourceUrl().openStream();
            xsr = getInputFactory().createXMLStreamReader(doc.getSourceUrl().toExternalForm(), inputStream);
        }
        // find the opening GateDocument tag
        xsr.nextTag();
        // parse the document
        try {
            DocumentStaxUtils.readGateXmlDocument(xsr, doc, statusListener);
        } finally {
            xsr.close();
            if (inputStream != null) {
                inputStream.close();
            }
            if (inputReader != null) {
                inputReader.close();
            }
        }
    } catch (XMLStreamException e) {
        doc.getFeatures().put("parsingError", Boolean.TRUE);
        Boolean bThrow = (Boolean) doc.getFeatures().get(GateConstants.THROWEX_FORMAT_PROPERTY_NAME);
        if (bThrow != null && bThrow.booleanValue()) {
            // error
            throw new DocumentFormatException(e);
        } else {
            Out.println("Warning: Document remains unparsed. \n" + "\n  Stack Dump: ");
            e.printStackTrace(Out.getPrintWriter());
        }
    // if
    } catch (IOException ioe) {
        throw new DocumentFormatException("I/O exception for " + doc.getSourceUrl().toString(), ioe);
    }
}

Example 3 with DocumentFormatException

use of gate.util.DocumentFormatException in project gate-core by GateNLP.

the class TikaFormat method unpackMarkup.

@Override
public void unpackMarkup(Document doc, RepositioningInfo repInfo, RepositioningInfo ampCodingInfo) throws DocumentFormatException {
    if (doc == null || doc.getSourceUrl() == null) {
        throw new DocumentFormatException("GATE document is null or no content found. Nothing to parse!");
    }
    // End if
    // Create a status listener
    StatusListener statusListener = new StatusListener() {

        @Override
        public void statusChanged(String text) {
            // This is implemented in DocumentFormat.java and inherited here
            fireStatusChanged(text);
        }
    };
    XmlDocumentHandler ch = new XmlDocumentHandler(doc, this.markupElementsMap, this.element2StringMap);
    Metadata metadata = extractParserTips(doc);
    ch.addStatusListener(statusListener);
    ch.setRepositioningInfo(repInfo);
    // set the object with ampersand coding positions
    ch.setAmpCodingInfo(ampCodingInfo);
    InputStream input = null;
    try {
        Parser tikaParser = new TikaConfig().getParser();
        input = doc.getSourceUrl().openStream();
        tikaParser.parse(input, ch, metadata, new ParseContext());
        setDocumentFeatures(metadata, doc);
    } catch (IOException e) {
        throw new DocumentFormatException(e);
    } catch (SAXException e) {
        throw new DocumentFormatException(e);
    } catch (TikaException e) {
        throw new DocumentFormatException(e);
    } finally {
        // null safe
        IOUtils.closeQuietly(input);
        ch.removeStatusListener(statusListener);
    }
    if (doc instanceof DocumentImpl) {
        ((DocumentImpl) doc).setNextAnnotationId(ch.getCustomObjectsId());
    }
}

Example 4 with DocumentFormatException

use of gate.util.DocumentFormatException in project gate-core by GateNLP.

the class NekoHtmlDocumentFormat method unpackMarkup.

/**
 * Unpack the markup in the document. This converts markup from the
 * native format into annotations in GATE format. If the document was
 * created from a String, then is recomandable to set the doc's
 * sourceUrl to <b>null</b>. So, if the document has a valid URL,
 * then the parser will try to parse the XML document pointed by the
 * URL.If the URL is not valid, or is null, then the doc's content
 * will be parsed. If the doc's content is not a valid XML then the
 * parser might crash.
 *
 * @param doc The gate document you want to parse. If
 *          <code>doc.getSourceUrl()</code> returns <b>null</b>
 *          then the content of doc will be parsed. Using a URL is
 *          recomended because the parser will report errors corectlly
 *          if the document is not well formed.
 */
@Override
public void unpackMarkup(Document doc, RepositioningInfo repInfo, RepositioningInfo ampCodingInfo) throws DocumentFormatException {
    if ((doc == null) || (doc.getSourceUrl() == null && doc.getContent() == null)) {
        throw new DocumentFormatException("GATE document is null or no content found. Nothing to parse!");
    }
    // End if
    // Create a status listener
    StatusListener statusListener = new StatusListener() {

        @Override
        public void statusChanged(String text) {
            // This is implemented in DocumentFormat.java and inherited here
            fireStatusChanged(text);
        }
    };
    boolean docHasContentButNoValidURL = hasContentButNoValidUrl(doc);
    NekoHtmlDocumentHandler handler = null;
    try {
        org.cyberneko.html.HTMLConfiguration parser = new HTMLConfiguration();
        // convert element and attribute names to lower case
        parser.setProperty("http://cyberneko.org/html/properties/names/elems", "lower");
        parser.setProperty("http://cyberneko.org/html/properties/names/attrs", "lower");
        // make parser augment infoset with location information
        parser.setFeature(NekoHtmlDocumentHandler.AUGMENTATIONS, true);
        // Create a new Xml document handler
        handler = new NekoHtmlDocumentHandler(doc, null, ignorableTags);
        // Register a status listener with it
        handler.addStatusListener(statusListener);
        // set repositioning object
        handler.setRepositioningInfo(repInfo);
        // set the object with ampersand coding positions
        handler.setAmpCodingInfo(ampCodingInfo);
        // construct the list of offsets for each line of the document
        int[] lineOffsets = buildLineOffsets(doc.getContent().toString());
        handler.setLineOffsets(lineOffsets);
        // set the handlers
        parser.setDocumentHandler(handler);
        parser.setErrorHandler(handler);
        // Parse the XML Document with the appropriate encoding
        XMLInputSource is;
        if (docHasContentButNoValidURL) {
            // no URL, so parse from string
            is = new XMLInputSource(null, null, null, new StringReader(doc.getContent().toString()), null);
        } else if (doc instanceof TextualDocument) {
            // textual document - load with user specified encoding
            String docEncoding = ((TextualDocument) doc).getEncoding();
            // XML, so no BOM stripping.
            URLConnection conn = doc.getSourceUrl().openConnection();
            InputStream uStream = conn.getInputStream();
            if ("gzip".equals(conn.getContentEncoding())) {
                uStream = new GZIPInputStream(uStream);
            }
            Reader docReader = new InputStreamReader(uStream, docEncoding);
            is = new XMLInputSource(null, doc.getSourceUrl().toString(), doc.getSourceUrl().toString(), docReader, docEncoding);
            // since we control the encoding, tell the parser to ignore any
            // meta http-equiv hints
            parser.setFeature("http://cyberneko.org/html/features/scanner/ignore-specified-charset", true);
        } else {
            // let the parser decide the encoding
            is = new XMLInputSource(null, doc.getSourceUrl().toString(), doc.getSourceUrl().toString());
        }
        /* The following line can forward an
       * ArrayIndexOutOfBoundsException from
       * org.cyberneko.html.HTMLConfiguration.parse and crash GATE.    */
        parser.parse(is);
        // Angel - end
        ((DocumentImpl) doc).setNextAnnotationId(handler.getCustomObjectsId());
    }/* Handle IOException specially.      */
     catch (IOException e) {
        throw new DocumentFormatException("I/O exception for " + doc.getSourceUrl().toString(), e);
    }/* Handle XNIException and ArrayIndexOutOfBoundsException:
     * flag the parsing error and keep going.     */
     catch (Exception e) {
        doc.getFeatures().put("parsingError", Boolean.TRUE);
        Boolean bThrow = (Boolean) doc.getFeatures().get(GateConstants.THROWEX_FORMAT_PROPERTY_NAME);
        if (bThrow != null && bThrow.booleanValue()) {
            // error
            throw new DocumentFormatException(e);
        } else {
            Out.println("Warning: Document remains unparsed. \n" + "\n  Stack Dump: ");
            e.printStackTrace(Out.getPrintWriter());
        }
    // if
    } finally {
        if (handler != null)
            handler.removeStatusListener(statusListener);
    }
// End if else try
}

Example 5 with DocumentFormatException

use of gate.util.DocumentFormatException in project gate-core by GateNLP.

the class SgmlDocumentFormat method unpackMarkup.

/**
 * Unpack the markup in the document. This converts markup from the
 * native format (e.g. SGML) into annotations in GATE format.
 * Uses the markupElementsMap to determine which elements to convert, and
 * what annotation type names to use.
 * The doc's content is first converted to a wel formed XML.
 * If this succeddes then the document is saved into a temp file and parsed
 * as an XML document.
 *
 * @param doc The gate document you want to parse.
 */
@Override
public void unpackMarkup(Document doc) throws DocumentFormatException {
    if ((doc == null) || (doc.getSourceUrl() == null && doc.getContent() == null)) {
        throw new DocumentFormatException("GATE document is null or no content found. Nothing to parse!");
    }
    // End if
    // Create a status listener
    StatusListener statusListener = new StatusListener() {

        @Override
        public void statusChanged(String text) {
            fireStatusChanged(text);
        }
    };
    XmlDocumentHandler xmlDocHandler = null;
    try {
        Sgml2Xml sgml2Xml = new Sgml2Xml(doc);
        fireStatusChanged("Performing SGML to XML...");
        // convert the SGML document
        String xmlUri = sgml2Xml.convert();
        fireStatusChanged("DONE !");
        // Out.println("Conversion done..." + xmlUri);
        // Out.println(sgml2Xml.convert());
        // Get a parser factory.
        SAXParserFactory saxParserFactory = SAXParserFactory.newInstance();
        // Set up the factory to create the appropriate type of parser
        // Set up the factory to create the appropriate type of parser
        // non validating one
        saxParserFactory.setValidating(false);
        // non namesapace aware one
        saxParserFactory.setNamespaceAware(true);
        // Create a SAX parser
        SAXParser parser = saxParserFactory.newSAXParser();
        // use it
        // create a new Xml document handler
        xmlDocHandler = new XmlDocumentHandler(doc, this.markupElementsMap, this.element2StringMap);
        // register a status listener with it
        xmlDocHandler.addStatusListener(statusListener);
        parser.parse(xmlUri, xmlDocHandler);
        ((DocumentImpl) doc).setNextAnnotationId(xmlDocHandler.getCustomObjectsId());
    } catch (ParserConfigurationException e) {
        throw new DocumentFormatException("XML parser configuration exception ", e);
    } catch (SAXException e) {
        throw new DocumentFormatException(e);
    } catch (IOException e) {
        throw new DocumentFormatException("I/O exception for " + doc.getSourceUrl().toString());
    } finally {
        if (xmlDocHandler != null)
            xmlDocHandler.removeStatusListener(statusListener);
    }
// End try
}